OmeSource

Classes

OmeSource

OME-compatible image source (base class)

Functions

get_resolution_from_pixel_size(→ tuple)
get_best_level_factor(→ tuple)
get_best_size(→ tuple)

Module Contents

class OmeSource.OmeSource

OME-compatible image source (base class)

metadata: dict

metadata dictionary

has_ome_metadata: bool

has ome metadata

dimension_order: str

source dimension order

output_dimension_order: str

data dimension order

source_pixel_size: list

original source pixel size

target_pixel_size: list

target pixel size

sizes: list

x/y size pairs for all pages

sizes_xyzct: list

xyzct size for all pages

pixel_types: list

pixel types for all pages

pixel_nbits: list

#bits for all pages

channels: list

channel information for all image channels

position: list

source position information

rotation: float

source rotation information

default_properties_order = 'xyzct'

default_physical_unit = 'µm'

_init_metadata(source_reference: str, source_pixel_size: list = None, target_pixel_size: list = None, source_info_required: bool = False)

_get_ome_metadata()

_init_sizes()

abstract get_source_dask()

get_mag() → float

get_dimension_order() → str

get_physical_size() → tuple

get_pixel_type(level: int = 0) → numpy.dtype

get_pixel_nbytes(level: int = 0) → int

get_channels() → list

get_size() → tuple

get_size_xyzct() → tuple

get_nchannels()

get_pixel_size() → list

get_pixel_size_micrometer()

get_position() → list

get_position_micrometer()

get_rotation() → float

get_shape(dimension_order: str = None, xyzct: tuple = None) → tuple

get_thumbnail(target_size: tuple, precise: bool = False) → numpy.ndarray

get_channel_window(channeli)

render(image: numpy.ndarray, source_dimension_order: str = None, t: int = 0, z: int = 0, channels: list = []) → numpy.ndarray

asarray(pixel_size: list = [], **slicing) → numpy.ndarray

asarray_um(**slicing)

asdask(chunk_size: tuple) → dask.array.Array

clone_empty() → numpy.ndarray

produce_chunks(chunk_size: tuple) → tuple

get_metadata() → dict

create_xml_metadata(output_filename: str, combine_rgb: bool = True, pyramid_sizes_add: list = None) → str

abstract _find_metadata()

abstract _asarray_level(level: int, **slicing) → numpy.ndarray

close()

OmeSource.get_resolution_from_pixel_size(pixel_size: list) → tuple

OmeSource.get_best_level_factor(source: OmeSource, target_pixel_size: list) → tuple

OmeSource.get_best_size(sizes: list, target_size: tuple) → tuple